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Samantha Riesenfeld

TitleAssistant Professor
InstitutionUniversity of Chicago
DepartmentPritzker Institute for Molecular Engineering
AddressChicago IL 60637
Email
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    Using high-throughput genomic data, Riesenfeld Group develops approaches to computationally infer the circuits that regulate gene expression and cellular function. By iterating experimental perturbations, data modeling, and targeted validations, they aim to extract from noisy, large-scale data the signals to help answer complex questions about the immune system, such as: What drives tolerant versus inflammatory immune responses? How do immune pathways contribute to or disrupt tissue homeostasis? How can immune responses be manipulated to restore health?

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    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Lisicka W, Earley ZM, Sifakis JJ, Erickson SA, Mattingly JR, Wu-Woods NJ, Krishnamurthy SR, Belkaid Y, Ismagilov RF, Cyster JG, Riesenfeld SJ, Bendelac A, Jabri B. Immunoglobulin A controls intestinal virus colonization to preserve immune homeostasis. Cell Host Microbe. 2025 Apr 09; 33(4):498-511.e10. PMID: 40154490.
      Citations:    Fields:    Translation:AnimalsCells
    2. Hieromnimon HM, Trzcinska A, Wen FT, Howard FM, Dolezal JM, Dyer E, Kochanny S, Schulte JJ, Wang C, Chen H, Chin J, Blair E, Agrawal N, Rosenberg A, Vokes E, Katipally R, Juloori A, Izumchenko E, Lingen MW, Cipriani N, Jalaly JB, Basu D, Riesenfeld SJ, Pearson AT. Analysis of AI foundation model features decodes the histopathologic landscape of HPV-positive head and neck squamous cell carcinomas. Oral Oncol. 2025 Apr; 163:107207. PMID: 40043423.
      Citations:    Fields:    Translation:HumansCells
    3. Sangani KA, Parker ME, Anderson HD, Chen L, Pandey SP, Pierre JF, Meisel M, Riesenfeld SJ, Hinterleitner R, Jabri B. Epigenetic control of commensal induced Th2 Responses and Intestinal immunopathology. bioRxiv. 2024 Aug 30. PMID: 39257820; PMCID: PMC11383986.
      Citations:    
    4. Liang Z, Anderson HD, Locher V, O'Leary C, Riesenfeld SJ, Jabri B, McDonald BD, Bendelac A. Eomes expression identifies the early bone marrow precursor to classical NK cells. Nat Immunol. 2024 Jul; 25(7):1172-1182. PMID: 38871999; PMCID: PMC11409033.
      Citations: 3     Fields:    Translation:AnimalsCells
    5. Ramesh S, Tomesh T, Riesenfeld SJ, Chong FT, Pearson AT. Quantum computing for oncology. Nat Cancer. 2024 Jun; 5(6):811-816. PMID: 38760645.
      Citations:    Fields:    Translation:Humans
    6. Gao CF, Vaikuntanathan S, Riesenfeld SJ. Dissection and integration of bursty transcriptional dynamics for complex systems. Proc Natl Acad Sci U S A. 2024 Apr 30; 121(18):e2306901121. PMID: 38669186; PMCID: PMC11067469.
      Citations: 5     Fields:    Translation:HumansAnimalsCells
    7. Gao CF, Vaikuntanathan S, Riesenfeld SJ. Dissection and Integration of Bursty Transcriptional Dynamics for Complex Systems. bioRxiv. 2023 Jun 13. PMID: 37398022; PMCID: PMC10312759.
      Citations:    
    8. Earley ZM, Lisicka W, Sifakis JJ, Kowalczyk A, Barlow JT, Shaw DG, Discepolo V, Tan IL, Gona S, Ernest JD, Matzinger P, Barreiro LB, Morgun A, Bendelac A, Ismagilov RF, Shulzhenko N, Riesenfeld SJ, Jabri B, Aguirre-Gamboa R. GATA4 controls regionalization of tissue immunity and commensal-driven immunopathology. Immunity. 2023 01 10; 56(1):43-57.e10. PMID: 36630917; PMCID: PMC10262782.
      Citations: 9     Fields:    Translation:HumansAnimalsCells
    9. Yang D, Jacobson A, Meerschaert KA, Sifakis JJ, Wu M, Chen X, Yang T, Zhou Y, Anekal PV, Rucker RA, Sharma D, Sontheimer-Phelps A, Wu GS, Deng L, Anderson MD, Choi S, Neel D, Lee N, Kasper DL, Jabri B, Huh JR, Johansson M, Thiagarajah JR, Riesenfeld SJ, Chiu IM. Nociceptor neurons direct goblet cells via a CGRP-RAMP1 axis to drive mucus production and gut barrier protection. Cell. 2022 10 27; 185(22):4190-4205.e25. PMID: 36243004; PMCID: PMC9617795.
      Citations: 56     Fields:    Translation:HumansAnimalsCells
    10. Pawlak M, DeTomaso D, Schnell A, Meyer Zu Horste G, Lee Y, Nyman J, Dionne D, Regan BML, Singh V, Delorey T, Schramm MA, Wang C, Wallrapp A, Burkett PR, Riesenfeld SJ, Anderson AC, Regev A, Xavier RJ, Yosef N, Kuchroo VK. Induction of a colitogenic phenotype in Th1-like cells depends on interleukin-23 receptor signaling. Immunity. 2022 09 13; 55(9):1663-1679.e6. PMID: 36070768; PMCID: PMC9808605.
      Citations: 15     Fields:    Translation:AnimalsCells
    11. Dani N, Herbst RH, McCabe C, Green GS, Kaiser K, Head JP, Cui J, Shipley FB, Jang A, Dionne D, Nguyen L, Rodman C, Riesenfeld SJ, Prochazka J, Prochazkova M, Sedlacek R, Zhang F, Bryja V, Rozenblatt-Rosen O, Habib N, Regev A, Lehtinen MK. A cellular and spatial map of the choroid plexus across brain ventricles and ages. Cell. 2021 05 27; 184(11):3056-3074.e21. PMID: 33932339; PMCID: PMC8214809.
      Citations: 125     Fields:    Translation:AnimalsCells
    12. Bielecki P, Riesenfeld SJ, Hütter JC, Torlai Triglia E, Kowalczyk MS, Ricardo-Gonzalez RR, Lian M, Amezcua Vesely MC, Kroehling L, Xu H, Slyper M, Muus C, Ludwig LS, Christian E, Tao L, Kedaigle AJ, Steach HR, York AG, Skadow MH, Yaghoubi P, Dionne D, Jarret A, McGee HM, Porter CBM, Licona-Limón P, Bailis W, Jackson R, Gagliani N, Gasteiger G, Locksley RM, Regev A, Flavell RA. Skin-resident innate lymphoid cells converge on a pathogenic effector state. Nature. 2021 04; 592(7852):128-132. PMID: 33536623; PMCID: PMC8336632.
      Citations: 88     Fields:    
    13. Xu H, Ding J, Porter CBM, Wallrapp A, Tabaka M, Ma S, Fu S, Guo X, Riesenfeld SJ, Su C, Dionne D, Nguyen LT, Lefkovith A, Ashenberg O, Burkett PR, Shi HN, Rozenblatt-Rosen O, Graham DB, Kuchroo VK, Regev A, Xavier RJ. Transcriptional Atlas of Intestinal Immune Cells Reveals that Neuropeptide a-CGRP Modulates Group 2 Innate Lymphoid Cell Responses. Immunity. 2019 10 15; 51(4):696-708.e9. PMID: 31618654; PMCID: PMC6991097.
      Citations: 116     Fields:    Translation:AnimalsCells
    14. Wallrapp A, Burkett PR, Riesenfeld SJ, Kim SJ, Christian E, Abdulnour RE, Thakore PI, Schnell A, Lambden C, Herbst RH, Khan P, Tsujikawa K, Xavier RJ, Chiu IM, Levy BD, Regev A, Kuchroo VK. Calcitonin Gene-Related Peptide Negatively Regulates Alarmin-Driven Type 2 Innate Lymphoid Cell Responses. Immunity. 2019 10 15; 51(4):709-723.e6. PMID: 31604686; PMCID: PMC7076585.
      Citations: 112     Fields:    Translation:AnimalsCells
    15. Wallrapp A, Riesenfeld SJ, Burkett PR, Kuchroo VK. Type 2 innate lymphoid cells in the induction and resolution of tissue inflammation. Immunol Rev. 2018 11; 286(1):53-73. PMID: 30294962; PMCID: PMC7370855.
      Citations: 23     Fields:    Translation:HumansAnimalsCells
    16. Wallrapp A, Riesenfeld SJ, Burkett PR, Abdulnour RE, Nyman J, Dionne D, Hofree M, Cuoco MS, Rodman C, Farouq D, Haas BJ, Tickle TL, Trombetta JJ, Baral P, Klose CSN, Mahlakõiv T, Artis D, Rozenblatt-Rosen O, Chiu IM, Levy BD, Kowalczyk MS, Regev A, Kuchroo VK. The neuropeptide NMU amplifies ILC2-driven allergic lung inflammation. Nature. 2017 09 21; 549(7672):351-356. PMID: 28902842; PMCID: PMC5746044.
      Citations: 306     Fields:    Translation:AnimalsCells
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